Committed step

Schematic representation of a metabolic branch point. The numbers represent chemical compounds, whereas the letters represent enzymes that catalyze the conversion indicated by the nearby arrow. In this scheme, enzyme c catalyzes the committed step in the biosynthesis of compound 6.

In enzymology, the committed step (also known as the firstcommitted step) is an effectively irreversibleenzymatic reaction that occurs at a branch point during the biosynthesis of some molecules.[1][2]
As the name implies, after this step, the molecules are "committed" to the pathway and will ultimately end up in the pathway's final product. The first committed step should not be confused with the rate-determining step, which is the slowest step in a reaction or pathway. However, it is sometimes the case that the first committed step is in fact the rate-determining step as well.[1]

Contents

Metabolic pathways require tight regulation so that the proper compounds get produced in the proper amounts. Often, the first committed step is regulated by processes such as feedback inhibition and activation. Such regulation ensures that pathway intermediates do not accumulate, a situation that can be wasteful or even harmful to the cell.

Examples of enzymes that catalyze the first committed steps of metabolic pathways[edit]

3-deoxy-D-arabinose-heptulsonate 7-phosphate synthase catalyses the first committed step of the shikimate pathway responsible for the synthesis of the aromatic amino acids Tyrosine, Tryptophan and Phenylalanine in plants, bacteria, fungi and some lower eukaryotes.

1.
Animal
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Animals are multicellular, eukaryotic organisms of the kingdom Animalia. The animal kingdom emerged as a clade within Apoikozoa as the group to the choanoflagellates. Animals are motile, meaning they can move spontaneously and independently at some point in their lives and their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later in their lives. All animals are heterotrophs, they must ingest other organisms or their products for sustenance, most known animal phyla appeared in the fossil record as marine species during the Cambrian explosion, about 542 million years ago. Animals can be divided broadly into vertebrates and invertebrates, vertebrates have a backbone or spine, and amount to less than five percent of all described animal species. They include fish, amphibians, reptiles, birds and mammals, the remaining animals are the invertebrates, which lack a backbone. These include molluscs, arthropods, annelids, nematodes, flatworms, cnidarians, ctenophores, the study of animals is called zoology. The word animal comes from the Latin animalis, meaning having breath, the biological definition of the word refers to all members of the kingdom Animalia, encompassing creatures as diverse as sponges, jellyfish, insects, and humans. Aristotle divided the world between animals and plants, and this was followed by Carl Linnaeus, in the first hierarchical classification. In Linnaeuss original scheme, the animals were one of three kingdoms, divided into the classes of Vermes, Insecta, Pisces, Amphibia, Aves, and Mammalia. Since then the last four have all been subsumed into a single phylum, in 1874, Ernst Haeckel divided the animal kingdom into two subkingdoms, Metazoa and Protozoa. The protozoa were later moved to the kingdom Protista, leaving only the metazoa, thus Metazoa is now considered a synonym of Animalia. Animals have several characteristics that set apart from other living things. Animals are eukaryotic and multicellular, which separates them from bacteria and they are heterotrophic, generally digesting food in an internal chamber, which separates them from plants and algae. They are also distinguished from plants, algae, and fungi by lacking cell walls. All animals are motile, if only at life stages. In most animals, embryos pass through a stage, which is a characteristic exclusive to animals. With a few exceptions, most notably the sponges and Placozoa and these include muscles, which are able to contract and control locomotion, and nerve tissues, which send and process signals

2.
Molecule
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A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. Molecules are distinguished from ions by their lack of electrical charge, however, in quantum physics, organic chemistry, and biochemistry, the term molecule is often used less strictly, also being applied to polyatomic ions. In the kinetic theory of gases, the molecule is often used for any gaseous particle regardless of its composition. According to this definition, noble gas atoms are considered molecules as they are in fact monoatomic molecules. A molecule may be homonuclear, that is, it consists of atoms of one element, as with oxygen, or it may be heteronuclear. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are not considered single molecules. Molecules as components of matter are common in organic substances and they also make up most of the oceans and atmosphere. Also, no typical molecule can be defined for ionic crystals and covalent crystals, the theme of repeated unit-cellular-structure also holds for most condensed phases with metallic bonding, which means that solid metals are also not made of molecules. In glasses, atoms may also be together by chemical bonds with no presence of any definable molecule. The science of molecules is called molecular chemistry or molecular physics, in practice, however, this distinction is vague. In molecular sciences, a molecule consists of a system composed of two or more atoms. Polyatomic ions may sometimes be thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i. e, according to Merriam-Webster and the Online Etymology Dictionary, the word molecule derives from the Latin moles or small unit of mass. Molecule – extremely minute particle, from French molécule, from New Latin molecula, diminutive of Latin moles mass, a vague meaning at first, the vogue for the word can be traced to the philosophy of Descartes. The definition of the molecule has evolved as knowledge of the structure of molecules has increased, earlier definitions were less precise, defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties. Molecules are held together by covalent bonding or ionic bonding. Several types of non-metal elements exist only as molecules in the environment, for example, hydrogen only exists as hydrogen molecule. A molecule of a compound is made out of two or more elements, a covalent bond is a chemical bond that involves the sharing of electron pairs between atoms

3.
Glycolysis
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Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy molecules ATP, glycolysis is a determined sequence of ten enzyme-catalyzed reactions. The intermediates provide entry points to glycolysis, for example, most monosaccharides, such as fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful, for example, the intermediate dihydroxyacetone phosphate is a source of the glycerol that combines with fatty acids to form fat. Glycolysis is an oxygen independent metabolic pathway, meaning that it not use molecular oxygen for any of its reactions. However the products of glycolysis are sometimes metabolized using atmospheric oxygen, when molecular oxygen is used for the metabolism of the products of glycolysis the process is usually referred to as aerobic, whereas if no oxygen is used the process is said to be anaerobic. Thus, glycolysis occurs, with variations, in all organisms. The wide occurrence of glycolysis indicates that it is one of the most ancient metabolic pathways, glycolysis could thus have originated from chemical constraints of the prebiotic world. Glycolysis occurs in most organisms in the cytosol of the cell, the most common type of glycolysis is the Embden–Meyerhof–Parnas, which was discovered by Gustav Embden, Otto Meyerhof, and Jakub Karol Parnas. Glycolysis also refers to other pathways, such as the Entner–Doudoroff pathway, however, the discussion here will be limited to the Embden–Meyerhof–Parnas pathway. The overall reaction of glycolysis is, The use of symbols in this equation makes it appear unbalanced with respect to oxygen atoms, hydrogen atoms, and charges. In the cellular environment, all three groups of ADP dissociate into −O− and H+, giving ADP3−, and this ion tends to exist in an ionic bond with Mg2+. ATP behaves identically except that it has four groups, giving ATPMg2−. When these differences along with the charges on the two phosphate groups are considered together, the net charges of −4 on each side are balanced. For simple fermentations, the metabolism of one molecule of glucose to two molecules of pyruvate has a net yield of two molecules of ATP, most cells will then carry out further reactions to repay the used NAD+ and produce a final product of ethanol or lactic acid. Many bacteria use inorganic compounds as hydrogen acceptors to regenerate the NAD+, cells performing aerobic respiration synthesize much more ATP, but not as part of glycolysis. These further aerobic reactions use pyruvate and NADH + H+ from glycolysis, the pathway of glycolysis as it is known today took almost 100 years to fully discover. The combined results of many experiments were required in order to understand the pathway as a whole

4.
Fertilisation
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The cycle of fertilisation and development of new individuals is called sexual reproduction. During double fertilisation in angiosperms the haploid male gamete combines with two polar nuclei to form a triploid primary endosperm nucleus by the process of vegetative fertilisation. In 1784, Spallanzani established the need of interaction between the females ovum and males sperm to form a zygote, oscar Hertwig, in Germany, described the fusion of nuclei of spermatozoa and of ova from sea urchin. In flowering plants there are two sperm from each pollen grain, in seed plants, after pollination, a pollen grain germinates, and a pollen tube grows and penetrates the ovule through a tiny pore called a micropyle. The sperm are transferred from the pollen through the pollen tube, bryophyte is a traditional name used to refer to all embryophytes that do not have true vascular tissue and are therefore called non-vascular plants. Some bryophytes do have specialised tissues for the transport of water, however, since these do not contain lignin, a fern is a member of a group of roughly 12,000 species of vascular plants that reproduce via spores and have neither seeds nor flowers. They differ from mosses by being vascular and they have stems and leaves, like other vascular plants. Most ferns have what are called fiddleheads that expand into fronds, the gymnosperms are a group of seed-producing plants that includes conifers, Cycads, Ginkgo, and Gnetales. The term gymnosperm comes from the Greek composite word γυμνόσπερμος, meaning naked seeds and their naked condition stands in contrast to the seeds and ovules of flowering plants, which are enclosed within an ovary. Gymnosperm seeds develop either on the surface of scales or leaves, often modified to form cones, the pollen tube does not directly reach the ovary in a straight line. It travels near the skin of the style and curls to the bottom of the ovary, then near the receptacle, it breaks through the ovule through the micropyle, after being fertilised, the ovary starts to swell and develop into the fruit. With multi-seeded fruits, multiple grains of pollen are necessary for syngamy with each ovule, the growth of the pollen tube is controlled by the vegetative cytoplasm. The sperms are interconnected and dimorphic, the one, in a number of plants, is also linked to the tube nucleus and the interconnected sperm. Double fertilisation is the process in angiosperms in which two sperm from each pollen tube fertilise two cells in a gametophyte that is inside an ovule. After the pollen tube enters the gametophyte, the tube nucleus disintegrates. This is the point when fertilisation actually occurs, pollination and fertilisation are two separate processes, the nucleus of the other sperm cell fuses with two haploid polar nuclei in the centre of the gametophyte. This triploid cell divides through mitosis and forms the endosperm, a nutrient-rich tissue, the two central-cell maternal nuclei that contribute to the endosperm arise by mitosis from the single meiotic product that also gave rise to the egg. Therefore, maternal contribution to the constitution of the triploid endosperm is double that of the embryo

5.
Enzyme inhibitor
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An enzyme inhibitor is a molecule that binds to an enzyme and decreases its activity. Since blocking an enzymes activity can kill a pathogen or correct a metabolic imbalance and they are also used in pesticides. The binding of an inhibitor can stop a substrate from entering the active site and/or hinder the enzyme from catalyzing its reaction. Inhibitor binding is reversible or irreversible. Irreversible inhibitors usually react with the enzyme and change it chemically and these inhibitors modify key amino acid residues needed for enzymatic activity. In contrast, reversible inhibitors bind non-covalently and different types of inhibition are produced depending on whether these inhibitors bind to the enzyme, many drug molecules are enzyme inhibitors, so their discovery and improvement is an active area of research in biochemistry and pharmacology. A medicinal enzyme inhibitor is often judged by its specificity and its potency, a high specificity and potency ensure that a drug will have few side effects and thus low toxicity. Enzyme inhibitors also occur naturally and are involved in the regulation of metabolism, for example, enzymes in a metabolic pathway can be inhibited by downstream products. This type of negative feedback slows the production line when products begin to build up and is an important way to maintain homeostasis in a cell, other cellular enzyme inhibitors are proteins that specifically bind to and inhibit an enzyme target. This can help control enzymes that may be damaging to a cell, a well-characterised example of this is the ribonuclease inhibitor, which binds to ribonucleases in one of the tightest known protein–protein interactions. Natural enzyme inhibitors can also be poisons and are used as defences against predators or as ways of killing prey, reversible inhibitors attach to enzymes with non-covalent interactions such as hydrogen bonds, hydrophobic interactions and ionic bonds. Multiple weak bonds between the inhibitor and the active site combine to produce strong and specific binding, in contrast to substrates and irreversible inhibitors, reversible inhibitors generally do not undergo chemical reactions when bound to the enzyme and can be easily removed by dilution or dialysis. There are four kinds of reversible enzyme inhibitors and they are classified according to the effect of varying the concentration of the enzymes substrate on the inhibitor. In competitive inhibition, the substrate and inhibitor cannot bind to the enzyme at the same time, as shown in the figure on the right. This usually results from the inhibitor having an affinity for the site of an enzyme where the substrate also binds. This type of inhibition can be overcome by high concentrations of substrate. However, the apparent Km will increase as it takes a higher concentration of the substrate to reach the Km point, competitive inhibitors are often similar in structure to the real substrate. In uncompetitive inhibition, the inhibitor binds only to the substrate-enzyme complex and this type of inhibition causes Vmax to decrease and Km to decrease

6.
Aspartate carbamoyltransferase
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Aspartate carbamoyltransferase catalyzes the first step in the pyrimidine biosynthetic pathway. In E. coli, the enzyme is a protein complex composed of 12 subunits. The composition of the subunits is C6R6, forming 2 trimers of catalytic subunits and 3 dimers of regulatory subunits, the particular arrangement of catalytic and regulatory subunits in this enzyme affords the complex with strongly allosteric behaviour with respect to its substrates. The enzyme is an example of allosteric modulation of fine control of metabolic enzyme reactions. ATCase does not follow Michaelis-Menten kinetics, but lies between the low-activity, low-affinity tense or T and the high-activity, high-affinity relaxed or R states, binding of ATP to the regulatory subunits results in an equilibrium shift towards the R state. ATCase controls the rate of pyrimidine biosynthesis by altering its catalytic velocity in response to levels of both pyrimidines and purines. The end-product of the pathway, CTP, decreases catalytic velocity, whereas ATP. Early studies demonstrated that ATCase consists of two different kinds of chains, which have different roles. These residues coordinate a zinc atom that is not involved in any catalytic property, the three-dimensional arrangement of the catalytic and regulatory subunits involves several ionic and hydrophobic stabilizing contacts between amino acid residues. Each catalytic chain is in contact with three other catalytic chains and two regulatory chains, each regulatory monomer is in contact with one other regulatory chain and two catalytic chains. In the unliganded enzyme, the two catalytic trimers are also in contact, the catalytic site of ATCase is located at the interface between two neighboring catalytic chains in the same trimer and incorporates amino acid side-chains from both of these subunits. Insight into the mode of binding of substrates to the center of ATCase was first made possible by the binding of a bisubstrate analogue. This compound is an inhibitor of ATCase and has a structure that is thought to be very close to that of the transition state of the substrates. Additionally, crystal structures of ATCase bound to carbamoylphosphate and succinate have been obtained, the active site is a highly positively charged pocket. Arg105, His134, and Thr55 help to increase the electrophilicity of the carbon by interacting with the carbonyl oxygen. The allosteric site in the domain of the R chains of the ATCase complex binds to the nucleotides ATP, CTP and/or UTP. There is one site with high affinity for ATP and CTP, ATP binds predominantly to the high-affinity sites and subsequently activates the enzyme, while UTP and CTP binding leads to inhibition of activity. UTP can bind to the site, but inhibition of ATCase by UTP is possible only in combination with CTP

7.
Phosphofructokinase 1
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Phosphofructokinase-1 is one of the most important regulatory enzymes of glycolysis. It is an enzyme made of 4 subunits and controlled by many activators and inhibitors. PFK-1 catalyzes the important committed step of glycolysis, the conversion of fructose 6-phosphate and ATP to fructose 1, 6-bisphosphate, glycolysis is the foundation for respiration, both anaerobic and aerobic. PFK is able to regulate glycolysis through allosteric inhibition, and in this way, for example, a high ratio of ATP to ADP will inhibit PFK and glycolysis. The key difference between the regulation of PFK in eukaryotes and prokaryotes is that in eukaryotes PFK is activated by fructose 2, the purpose of fructose 2, 6-bisphosphate is to supersede ATP inhibition, thus allowing eukaryotes to have greater sensitivity to regulation by hormones like glucagon and insulin. Mammalian PFK1 is a 340kd tetramer composed of different combinations of three types of subunits, muscle, liver, and platelet, the composition of the PFK1 tetramer differs according to the tissue type it is present in. For example, mature muscle expresses only the M isozyme, therefore, the liver and kidneys express predominantly the L isoform. In erythrocytes, both M and L subunits randomly tetramerize to form M4, L4 and the three forms of the enzyme. As a result, the kinetic and regulatory properties of the various isoenzymes pools are dependent on subunit composition, tissue-specific changes in PFK activity and isoenzymic content contribute significantly to the diversities of glycolytic and gluconeogenic rates which have been observed for different tissues. PFK1 is an enzyme and has a structure similar to that of hemoglobin in so far as it is a dimer of a dimer. One half of each contains the ATP binding site whereas the other half the substrate binding site as well as a separate allosteric binding site. Each subunit of the tetramer is 319 amino acids and consists of two domain, one that binds the substrate ATP, and the other that binds fructose-6-phosphate, each domain is a b barrel, and has cylindrical b sheet surrounded by alpha helices. On the opposite side of the each subunit from each site is the allosteric site. ATP and AMP compete for this site, F6P binds with a high affinity to the R state but not the T state enzyme. For every molecule of F6P that binds to PFK1, the enzyme progressively shifts from T state to the R state, thus a graph plotting PFK1 activity against increasing F6P concentrations would adopt the sigmoidal curve shape traditionally associated with allosteric enzymes. PFK1 belongs to the family of phosphotransferases and it catalyzes the transfer of γ-phosphate from ATP to fructose-6-phosphate, the PFK1 active site comprises both the ATP-Mg2+ and the F6P binding sites. Some proposed residues involved with substrate binding in E. coli PFK1 include Asp127, in the T state, enzyme conformation shifts slightly such that the space previously taken up by the Arg162 is replaced with Glu161. This swap in positions between adjacent amino acid residues inhibits the ability of F6P to bind the enzyme, allosteric activators such as AMP and ADP bind to the allosteric site as to facilitate the formation of the R state by inducing structural changes in the enzyme

8.
Negative feedback
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Whereas positive feedback tends to lead to instability via exponential growth, oscillation or chaotic behavior, negative feedback generally promotes stability. Negative feedback tends to promote a settling to equilibrium, and reduces the effects of perturbations, Negative feedback loops in which just the right amount of correction is applied with optimum timing can be very stable, accurate, and responsive. General negative feedback systems are studied in control systems engineering, in the invisible hand of the market metaphor of economic theory, reactions to price movements provide a feedback mechanism to match supply and demand. In centrifugal governors, negative feedback is used to maintain a near-constant speed of an engine, in a Steering engine, power assistance is applied to the rudder with a feedback loop, to maintain the direction set by the steersman. In servomechanisms, the speed or position of an output, as determined by a sensor, is compared to a set value, and any error is reduced by negative feedback to the input. In analog computing feedback around operational amplifiers is used to generate mathematical functions such as addition, subtraction, integration, differentiation, logarithm, in a phase locked loop feedback is used to maintain a generated alternating waveform in a constant phase to a reference signal. In many implementations the generated waveform is the output, but when used as a demodulator in a FM radio receiver, if there is a frequency divider between the generated waveform and the phase comparator, the device acts as a frequency multiplier. In organisms, feedback enables various measures to be maintained within a range by homeostatic processes. Negative feedback as a technique may be seen in the refinements of the water clock introduced by Ktesibios of Alexandria in the 3rd century BCE. Self-regulating mechanisms have existed since antiquity, and were used to maintain a constant level in the reservoirs of water clocks as early as 200 BCE, Negative feedback was implemented in the 17th Century. The term feedback was well established by the 1920s, in reference to a means of boosting the gain of an electronic amplifier, friis and Jensen described this action as positive feedback and made passing mention of a contrasting negative feed-back action in 1924. Karl Küpfmüller published papers on an automatic gain control system. Nyquist and Bode built on Black’s work to develop a theory of amplifier stability, early researchers in the area of cybernetics subsequently generalized the idea of negative feedback to cover any goal-seeking or purposeful behavior. All purposeful behavior may be considered to require negative feed-back, for understanding the general principles of dynamic systems, therefore, the concept of feedback is inadequate in itself. What is important is that complex systems, richly cross-connected internally, have complex behaviors, to reduce confusion, later authors have suggested alternative terms such as degenerative, self-correcting, balancing, or discrepancy-reducing in place of negative. In many physical and biological systems, qualitatively different influences can oppose each other, for example, in biochemistry, one set of chemicals drives the system in a given direction, whereas another set of chemicals drives it in an opposing direction. If one or both of these influences are non-linear, equilibrium point result. In biology, this process is referred to as homeostasis, whereas in mechanics

9.
Enzyme catalysis
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Enzyme catalysis is the increase in the rate of a chemical reaction by the active site of a protein. The protein catalyst may be part of a complex, and/or may transiently or permanently associate with a Cofactor. Catalysis of biochemical reactions in the cell is vital due to the very low rates of the uncatalysed reactions at room temperature and pressure. A key driver of protein evolution is the optimization of such catalytic activities via protein dynamics, the mechanism of enzyme catalysis is similar in principle to other types of chemical catalysis. By providing an alternative reaction route the enzyme reduces the required to reach the highest energy transition state of the reaction. The reduction of activation increases the amount of reactant molecules that achieve a sufficient level of energy, such that they reach the activation energy. As with other catalysts, the enzyme is not consumed during the reaction but is recycled such that a single enzyme performs many rounds of catalysis, the favored model for the enzyme-substrate interaction is the induced fit model. The advantages of the induced fit mechanism arise due to the effect of strong enzyme binding. There are two different mechanisms of substrate binding, uniform binding, which has strong binding, and differential binding. The stabilizing effect of uniform binding increases both substrate and transition state binding affinity, while differential binding increases only transition state binding affinity, both are used by enzymes and have been evolutionarily chosen to minimize the activation energy of the reaction. It is important to clarify, however, that the induced fit concept cannot be used to rationalize catalysis and that is, the chemical catalysis is defined as the reduction of Ea‡ relative to Ea‡ in the uncatalyzed reaction in water. The induced fit only suggests that the barrier is lower in the form of the enzyme. Induced fit may be beneficial to the fidelity of molecular recognition in the presence of competition, →→→editor These conformational changes also bring catalytic residues in the active site close to the chemical bonds in the substrate that will be altered in the reaction. After binding takes place, one or more mechanisms of catalysis lowers the energy of the transition state. This effect is analogous to an increase in concentration of the reagents. The binding of the reagents to the enzyme gives the reaction intramolecular character, however, the situation might be more complex, since modern computational studies have established that traditional examples of proximity effects cannot be related directly to enzyme entropic effects. Also, the original proposal has been found to largely overestimate the contribution of orientation entropy to catalysis. Histidine is often the residue involved in these reactions, since it has a pKa close to neutral pH

10.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase

11.
Metabolic pathway
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In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of a reaction are known as metabolites. In a metabolic pathway, the product of one acts as the substrate for the next. These enzymes often require dietary minerals, vitamins, and other cofactors to function, different metabolic pathways function based on the position within a eukaryotic cell and the significance of the pathway in the given compartment of the cell. For instance, the citric cycle, electron transport chain. In contrast, glycolysis, pentose phosphate pathway, and fatty acid biosynthesis all occur in the cytosol of a cell, the two pathways complement each other in that the energy released from one is used up by the other. The degradative process of a catabolic pathway provides the required to conduct a biosynthesis of an anabolic pathway. In addition to the two distinct metabolic pathways is the pathway, which can be either catabolic or anabolic based on the need for or the availability of energy. The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use, metabolic pathways are often considered to flow in one direction. Although all chemical reactions are reversible, conditions in the cell are often such that it is thermodynamically more favorable for flux to flow in one direction of a reaction. For example, one pathway may be responsible for the synthesis of an amino acid. One example of an exception to rule is the metabolism of glucose. Glycolysis results in the breakdown of glucose, but several reactions in the pathway are reversible. Glycolysis was the first metabolic pathway discovered, As glucose enters a cell, metabolic pathways are often regulated by feedback inhibition. Some metabolic pathways flow in a cycle wherein each component of the cycle is a substrate for the subsequent reaction in the cycle, the net reaction is, therefore, thermodynamically favorable, for it results in a lower free energy for the final products. A catabolic pathway is a system that produces chemical energy in the form of ATP, GTP, NADH, NADPH, FADH2, etc. from energy containing sources such as carbohydrates, fats. The end products are carbon dioxide, water, and ammonia. Coupled with an reaction of anabolism, the cell can synthesize new macromolecules using the original precursors of the anabolic pathway

12.
Peptidoglycan
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Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β- linked N-acetylglucosamine, attached to the N-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be cross-linked to the chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a role in the bacterial cell wall, giving structural strength. Peptidoglycan is also involved in binary fission during bacterial cell reproduction, the peptidoglycan layer is substantially thicker in gram-positive bacteria than in gram-negative bacteria, with the attachment of the S-layer. Peptidoglycan forms around 90% of the dry weight of gram-positive bacteria, thus, presence of high levels of peptidoglycan is the primary determinant of the characterisation of bacteria as gram-positive. In gram-positive strains, it is important in attachment roles and serotyping purposes, for both gram-positive and gram-negative bacteria, particles of approximately 2 nm can pass through the peptidoglycan. The peptidoglycan layer in the cell wall is a crystal lattice structure formed from linear chains of two alternating amino sugars, namely N-acetylglucosamine and N-acetylmuramic acid. The alternating sugars are connected by a β--glycosidic bond, peptidoglycan is one of the most important sources of D-amino acids in nature. Cross-linking between amino acids in different linear amino sugar chains occurs with the help of the enzyme DD-transpeptidase and results in a 3-dimensional structure that is strong, the specific amino acid sequence and molecular structure vary with the bacterial species. The peptidoglycan monomers are synthesized in the cytosol and are attached to a membrane carrier bactoprenol. Bactoprenol transports peptidoglycan monomers across the membrane where they are inserted into the existing peptidoglycan. In the first step of peptidoglycan synthesis, the glutamine, which is an acid, donates an amino group to a sugar. This turns fructose 6-phosphate into glucosamine-6-phosphate, in step two, an acetyl group is transferred from acetyl CoA to the amino group on the glucosamine-6-phosphate creating N-acetyl-glucosamine-6-phosphate. In step three of the process, the N-acetyl-glucosamine-6-phosphate is isomerized, which will change N-acetyl-glucosamine-6-phosphate to N-acetyl-glucosamine-1-phosphate. In step 4, the N-acetyl-glucosamine-1-phosphate, which is now a monophosphate, uridine triphosphate, which is a pyrimidine nucleotide, has the ability to act as an energy source. In this particular reaction, after the monophosphate has attacked the UTP and this initial stage, is used to create the precursor for the NAG in peptidoglycan. In step 5, some of the UDP-N-acetylglucosamine is converted to UDP-MurNAc by the addition of a group to the glucosamine

The energies of the stages of a chemical reaction. Uncatalysed (dashed line), substrates need a lot of activation energy to reach a transition state, which then decays into lower-energy products. When enzyme catalysed (solid line), the enzyme binds the substrates (ES), then stabilizes the transition state (ES‡) to reduce the activation energy required to produce products (EP) which are finally released.

In science, a process that is not reversible is called irreversible. This concept arises frequently in thermodynamics. …

Irreversible adiabatic process: If the cylinder is a perfect insulator, the initial top-left state cannot be reached anymore after it is changed to the one on the top-right. Instead, the state on the bottom left is assumed when going back to the original pressure because energy is converted into heat.